DNA as a Biometric Identifier

1. DNA as a Biometric Identifier Presented by: Shannon Soltysiak Hamed Valizadegan

2. DNA, a biometric? DNA differs from standard biometrics in several ways: • DNA requires a tangible physical sample as opposed to an impression, image, or recording. • DNA matching is not done in real-time, and currently not all stages of comparison are automated. • DNA matching does not employ templates or feature extraction, but rather represents the comparison of actual samples.

3. Why DNA? • DNA is unique to every individual on the planet • Only identical twins share the same DNA • It can be easily obtained from a variety of sources • It is readily used in forensics to match crime scene evidence to individuals • It does not change during the life!

4. Paper or plastic cup Glass Ear wax Fingernail clippings Socks Urine Licked stamps Cheek swabs Sweaty t-shirts Hair with roots Hair without roots DNA Sources • Dried blood • Whole blood • Chewed gum • Dental floss • Cigarette butts • Used tissue • Dried skin • Used razor • Other biological specimens

5. DNA Basics Think back to high school biology! • Double-stranded helical molecule resembling a twisted ladder • Sugar and phosphate backbone and nucleic acid interior • Found in the nucleus of all cells (there is also DNA in the mitochondria of cells) • Bundled into chromosomes • Chromosomes replicate each time a cell divides

6. A T A G G C T A T T T C A DNA Basic (con’t) • Only 4 nucleic acids (nucleotides) comprise the genetic code of DNA • (A)denine • (C)ytosine • (T)hymine • (G)uanine • Base Pairing! A-T and G-C • 3 billion such the pairs in DNA T A T C C G A T A A A G T http://www.don-lindsay-archive.org/creation/dna.jpg

7. DNA Replication http://www.genelex.com/paternitytesting/images/dna-molecule.jpg During replication, the two DNA strands separate, or denature, and a new complementary strand is constructed using the exposed bases as a template!

8. Human DNA • Humans have 23 homologous (“pairs of”) chromosomes resulting in 46 total • One set of 23 from each parent is passed on to offspring. • 99.7% of human DNA is shared. • 0.3% (~ 1 million nucleotides) is variable! • This variability is inherited and is therefore unique to each individual. • These variable regions, called Short Tandem Repeats (or STRs), can be examined to distinguish one person from another.

9. http://www.mtsinai.on.ca/pdmg/images/chromosome.jpg

10. STRs (Short Tandem Repeats) • In order to distinguish one person from another using DNA, you need highly variable segments of DNA. • In the early 1980s, several highly variable regions were discovered that could be used to tell individuals apart! • Today, there are 13 such regions that are used in DNA profiling.

11. How do STRs work? • At each of the 13 regions (or loci), there is a repeated sequence that is variable in length between individuals. • ACCT repeated at one locus, or TTTC repeated at another • The number of repeats at each location can be measured during DNA sequencing. • Each number of repeats has statistics associated with it that can be compared to the population. • The Product Rule can be used to multiply the statistics for all 13 regions, yielding a highly individualizing result. • Most DNA profiles give odds of sharing a profile with another person on earth as about one in a trillion!

12. Example STR result for a single locus http://www.rechtsmedizin.uni-mainz.de/Remedneu/molgen/Repeat.jpg

14. Cracking the DNA code! 3 Important Steps: • Extract (obtain and isolate DNA from sample) • Amplify (create multiple copies of the “target sequences”) • Sequence (obtain unique code of nucleic acid bases from the DNA sample) ***Contamination at any of these steps will result in test failure!!!***

15. DNA Extraction Main Methods of Extraction: • Organic • Chelex™ • FTA™ paper (or similar) • Alkaline

16. DNA Extraction Methods • Organic • Uses a phenol, chloroform, and several centrifuge steps to separate DNA from cellular debris. • Time: 2-3 hours • Chelex™ • Uses a boiling step and iminodiacetic beads to bind DNA. • Quick, but also not very clean and prone to degradation • Time: less than one hour

17. DNA Extraction Methods (con’t) • FTA™ paper • Sample placed directly on paper, allowed to dry, and is washed several times. • Paper can then proceed directly to amplification reaction. • Time: less than an hour • Alkaline • Sample is dissolved in a strong base such as sodium hydroxide and the DNA is removed via filtering • Time: several hours

18. DNA Amplification • After DNA is isolated from a biological sample, the number of copies must be increased • DNA must be amplified before proper sequencing can be carried out to ensure enough is present for the reaction

19. Polymerase Chain Reaction (PCR) • PCR is an enzymatic amplification of DNA. • PCR exponentially increases the initial copy number of DNA. • The reaction requires extracted DNA, primers, a polymerase (the enzyme), free-floating nucleotide bases, and buffer. • These ingredients, along with a series of temperature increases and decreases, allows for rapid, accurate replication of DNA. • TIME: 2-3 hours for 32 cycles

20. Polymerase Chain Reaction http://bcs.whfreeman.com/thelifewire/content/chp11/f11020.gif

21. DNA Sequencing • DNA sequencing is the step that generates a DNA profile. • Amplified DNA is loaded into the genetic analyzer (sequencer) with fluorescently labeled A, T, C, and Gs attached to the DNA • An electric current is applied to the system and the DNA migrates past a laser—the bases that pass by the laser are recorded, one at a time, until the entire sequence is recorded. • Once the data are analyzed, a unique DNA profile can be visualized • TIME: ~30 minutes per sample

22. Common Genetic Analyzers ABI 310 Hitachi FMBIO II http://www.helixxtec.com/Hitachi/fmbio.htm http://www.appliedbiosystems.com/catalog/myab/StoreCatalog/products/CategoryDetails.jsp?hierarchyID=102&category1st=a50&category2nd=a51&category3rd=111903

23. http://images.google.com/imgres?imgurl=http://www.forensic.gov.uk/forensic_t/inside/dna_profile/images/dna_22.jpg&imgrefurl=http://www.forensic.gov.uk/forensic_t/inside/dna_profile/&h=350&w=466&sz=18&tbnid=ip3f7602C14J:&tbnh=93&tbnw=124&start=4&prev=/images%3Fq%3DDNA%2Bprofile%26hl%3Den%26lr%3D http://images.google.com/imgres?imgurl=http://www.forensic.gov.uk/forensic_t/inside/dna_profile/images/dna_22.jpg&imgrefurl=http://www.forensic.gov.uk/forensic_t/inside/dna_profile/&h=350&w=466&sz=18&tbnid=ip3f7602C14J:&tbnh=93&tbnw=124&start=4&prev=/images%3Fq%3DDNA%2Bprofile%26hl%3Den%26lr%3D

24. DNA Profiling Timeline • Obtaining a sample such as a swab of cheek cells (buccal swab): ~10 seconds • Extracting DNA: 30minutes – 3 hours • Amplifying DNA: 2 – 3 hours • Sequencing DNA: 30 min – 1 hour Total: minimum of approximately 3 hours This is unacceptable for biometric use! What can be done??

25. Advances in DNA Technology • Extracting DNA • New commercial products are available that allow for the rapid collection and extraction of DNA • The Bode Technologies Buccal DNA Collector functions similarly to FTA™ paper • A scraping of cheek cells can be collected and transferred directly to the PCR reaction tube for amplification, greatly reducing extraction time TIME: less than 30 seconds

26. Advances in DNA Technology • Amplifying DNA • Products in the research stage can amplify DNA in minutes rather than hours! • The new devices rapidly change temperature, allowing DNA to be copied at a much quicker rate • MATCI (Miniature Analytical Thermal Cycling Instrument) is a portable PCR unit that can perform 32 cycles in about 21 minutes! • On-chip PCR utilizes glass microchips with sample chambers to perform PCR TIME: approximately 20 minutes

27. MATCI device http://aafs.micronexx.com/PDF/JOFS/JFSCH8315X3/JFSCH8315X3.pdf

28. Advances in DNA Technology • Sequencing DNA • High-throughput DNA analysis is commercially available with products like the ABI 3730xl. • Microchip sequencers in the research phase have small channels etched in them that perform the DNA separation and laser detection. • The small distance (~2cm) the DNA travels (opposed to 35cm in standard machines) allows results in as little as 30 seconds • High-throughput microchips have also been shown to provide results up to 5 times faster than current machines (Paegel et al.)

29. Nanochip™ Microchip ABI 3730xl http://www.appliedbiosystems.com/catalog/myab/StoreCatalog/products/CategoryDetails.jsp?hierarchyID=102&category1st=a50&category2nd=a51&category3rd=111907 http://www.kpl.gov.tr/image/dnachip11.jpg

30. Advances in DNA Technology • New research in microchip technology is aiming to combine DNA amplification and sequencing! • Adding DNA extraction to the continuous flow microchip is also in the works • Combining all three steps to obtain a DNA profile is the DNA profiling method of the future, and the one that is most applicable to biometrics

31. Timeline with new technology • Obtaining a sample such as a swab of cheek cells (buccal swab): 10 seconds • Extracting DNA: ~10 seconds • Amplifying DNA: ~20 minutes • Sequencing DNA: 30 seconds – 5 minutes Total: Less than 30 minutes!

32. Matching DNA Profiles • CODIS • The CODIS System currently in place by the FBI is similar to AFIS • Convicted offenders’ DNA profiles are loaded into the system to catch repeat offenders and those that commit crimes across state lines • Simple matching is the algorithm used to compare profiles • A database such as CODIS would be ideal for a biometric DNA database

33. To Summarize… • DNA is highly individualizing and has great potential as a biometric identifier • The nature of DNA and the state of current technology prevents DNA from being an efficient biometric • New technology and current research have greatly reduced the time required to generate a DNA profile • Despite the current advances, DNA profiling as a means of biometric identification still falls short of current demand